Molecule Tutorials - Herong's Tutorial Examples

∟PyMol Editing Functions

∟"remove pk*" and "remove_picked" Commands

This section provides a tutorial on how to remove atoms from a molecule in PyMol using picked atoms as special selections, pk1, pk2, pk3 and pk4.

Once atoms are picked and labeled as "pk1", "pk2", "pk3" and "pk4" selections, you can use "remove pk*" or "remove_picked" commands to remove picked atoms from the molecule structure. For example: 

PyMOL># remove the first picked atom
PyMOL>remove pk1

PyMOL># remove the all picked atoms
PyMOL>remove_picked

You can also click "Build > Remove (pk1)" from the menu to remove the first picked atom.

MyMol Remove pk1 (First Picked Atom)
MyMol Remove pk1 (First Picked Atom)

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 DNA Sequencing

 Gene Mutation

 SDF (Structure Data File)

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

►PyMol Editing Functions

 "pk1", "pk2", "pk3" and "pk4" Selections

 "edit id n1, id n2, id n3, id n4" Commands

►"remove pk*" and "remove_picked" Commands

 "unbond pk1, pk2" and "bond pk1, pk2" Commands

 "replace new_atom, ..." Replace pk1 with New Atom

 "attach new_atom, ..." Attach to pk1 with New Atom

 Build Alcohol Molecule with PyMol

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 HGNC (HUGO Gene Nomenclature Committee)

 Relocated Tutorials

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB